The present invention concerns muteins of avidin and streptavidin with a reduced binding affinity for biotin as well as their use as interference elimination reagents in methods for the determination of an analyte e.g. in diagnostic tests such as immunoassays and nucleic acid hybridization assays. In addition the invention concerns the use of muteins of avidin and streptavidin as systems that can be regenerated for binding biotin for example for the analysis of biotinylated molecules, for investigating receptor-ligand interactions as well as for the affinity purification of biotinylated molecules.
In detection methods for the determination of analytes such as immunoassays and nucleic acid hybridization assays the analytes are often determined by means of high affinity interaction between the partners of a specific binding pair. A typical example for a specific binding pair is the avidin/streptavidin-biotin complex. When using the avidin/streptavidin-biotin binding pair its high binding affinity is used. In this process a solid phase coated with avidin/streptavidin is for example used to which a biotinylated complex of analyte and specific receptor can bind. In other test formats avidin/streptavidin can also be used in a soluble form.
However, apart from specific interactions. side reactions often also occur such as for example undesired interactions and unspecific binding reactions between the test components and additional components present in the sample or on the solid phase. In particular other substances present in the sample often bind to immobilized or soluble avidin and streptavidin and thereby cause false positive or false negative test results. Furthermore these interactions can also cause an increase in the background signal and an increased scattering of the signals which decreases the sensitivity and specificity of the respective test.
Various attempts have been made to reduce these unspecific interactions. Thus it is for example known that various carbohydrate components and various proteins, protein mixtures or protein fractions and their hydrolysates can reduce unspecific interactions between the test components and the analyte in immunoassays (Robertson et al., J. of Immun. Med. 26 (1985) 195; EP-A-260 903; U.S. Pat. No. 4,931,385). However, the use of such carbohydrate and protein components has the disadvantage that components contained therein can cause additional interferences in the test. Enzymatically produced hydrolysates can in addition be contaminated by proteases used in their production and as a rule do not have a uniform quality since the cleavage is difficult to control. Such protease impurities can attack test components and already in small amounts lead to impairment of test function and storage stability.
Furthermore the use of chemically modified proteins especially of succinylated or acetylated proteins (U.S. Pat. No. 5,051,356; EP-A-0 525 916) has also been described to reduce unspecific interactions. However, it is not possible with these substances to avoid many of the false positive or false negative results in tests for antibodies from serum.
In order to avoid unspecific interactions it has additonally been proposed that ultrafine particles be added to the test reagents with a maximum average size of 0.2 xcexcm which are formed in such a way that they bind to interfering components and capture them (EP 0 163 312). However, this requires a special preparation of these ultrafine particles and in addition the type of unspecific factors present in the sample must be known.
In DE-A-44 07 423 and DE-A-44 34 093 it has been proposed that interferences which occur due to unspecific interactions between sample components and a streptavidin-coated solid phase be eliminated by means of a pre-reaction. The pre-reaction is advantageously carried out on a solid phase which is as similar as possible to the active streptavidin-coated solid phase but to which the sample molecules cannot bind specifically. In contrast unspecific components also bind to the inactive solid phase and can therefore be removed.
According to DE-A-44 07 423 streptavidin can be inactivated by covalent derivatization or covalent modification. However, a disadvantage is that this requires a time-consuming subsequent chemical modification. Moreover, chemical derivatization can change the region around the active centre of the native streptavidin in an undesired manner which reduces the interference elimination effects and may even lead to additional interfering interactions. Interference by unspecific interactions which occur at the biotin binding pocket cannot be eliminated by covalent modifications.
The avidin/streptavidin-biotin system is the subject matter of several investigations due to the strong, non-covalent affinity of the binding partners (KA about 1015 l/mol). The high binding affinity has mainly been attributed to interactions between tryptophan residues of streptavidin and biotin. However, a significant decrease of the binding affinity of streptavidin variants to iminobiotin could be achieved by modifying the tryptophan residues (Chilkoti et al., Proc. Natl. Acad. Sci. USA 92 (1995) 1754-1758, Sano and Cantor, Proc. Natl. Acad. Sci. USA 92 (1995) 3180-3184). However, it was not possible to unequivocally demonstrate a reduction of the binding affinity to biotin (cf. Chilkoti et al., Supra, FIGS. 1A and 1B). Such variants are therefore unsuitable for use as interference elimination reagents since they can also specifically react with biotinylated test components due to their still very high binding affinity.
The object of the present invention was therefore to provide a reagent by means of which interfering influences on detection methods for the determination of an analyte e.g. immunoassays or nucleic acid hybridization assays can be reduced.
This object is achieved according to the invention by a polypeptide capable of binding to biotin selected from muteins of avidin and streptavidin wherein the mutein (a) differs from the native polypeptide by at least one amino acid and (b) has a binding affinity to biotin of less than 1010 l/mol.
The binding affinity for the reaction streptavidin/biotin complex⇄streptavidin+biotin is about 1015 l/mol. The streptavidin/biotin system used as a capture system is thus provided with one of the strongest known non-covalent interactions between a protein and a ligand. Surprisingly it was found that a polypeptide is obtained by substitution of one or several amino acids of streptavidin or avidin which on the one hand can be renatured when produced recombinantly and on the other hand enables the binding affinity to biotin to be reduced to  less than 1010 l/mol, furthermore the muteins according to the invention preferably having a structure which corresponds to the structure of the active polypeptide. The muteins according to the invention preferably have a high immunological cross-reactivity with the native polypeptide. In addition it is preferable that they are able to dimerize or tetramerize. Surprisingly the muteins like native streptavidin or avidin are able to bind to interfering sample components as they can occur in biological samples e.g. in body fluids such as serum, plasma, whole blood etc. despite the reduced binding affinity to biotin.
Due to their special properties the muteins according to the invention can be used for various applications. A lowering of the binding affinity is synonymous to lowering the interactions between biotin and the muteins. Muteins according to the invention can be designed in such a way that they under no circumstances bind to biotin or that a relatively loose reversible binding is present. Since the spatial structure of the muteins is preferably not significantly changed in comparison to the native polypeptide, interactions with other substances are not affected. A reagent is obtained in this way which corresponds in its spatial structure and its binding properties to native streptavidin or avidin with the exception of the modified binding capacity to biotin.
Aqueous samples can in general be used as test samples. In particular biological samples such as body fluids such e.g. whole blood, blood plasma, serum, saliva, tissue fluid, liquor or urine are used.
The substitution of various amino acids by mutagenesis allows a defined production of muteins. In contrast to other modifications of streptavidin such as for example chemical derivatization the structure of the muteins according to the invention is retained. Thus no interfering interactions between additionally introduced derivatization reagents and components of the sample to be tested can occur.
The binding affinity of the muteins according to the invention to biotin is preferably  less than 109 l/mol, more preferably  less than 108 l/mol even more preferably  less than 107 l/mol, especially preferably  less than 106 l/mol and most preferably  less than 105 l/mol.
Streptavidin or avidin muteins according to the invention can preferably be regenerated when immobilized on a sensor chip surface such as a BIAcore surface.
In the case of a streptavidin mutein it is preferable to substitute one or several amino acids at positions Leu25, Ser27, Tyr43, Ser45, Val47, Gly48, Ser88, Thr90, Leu110 or/and Asp128 by another amino acid. The binding capacity of biotin can be reduced by substituting one amino acid with a small residue by an amino acid with a larger residue for example by substituting Leu or Ser by Trp, Arg, Tyr, Phe or His. In addition the binding ability of biotin can also be reduced or blocked by an additionally introduced disulfide bridge which decreases the accessibility of the biotin binding pocket. An additional disulfide bridge can for example be formed by substituting two amino acids by two cysteines at a correct spatial distance. It is also possible to reduce the biotin binding ability by additional ionic interactions. For this a positively charged amino acid such as Arg or Lys can for example be introduced which forms ionic interactions with Asp128. On the other hand it is also possible to introduce a positively charged and a negatively charged amino acid which can form a salt bridge with one another and can thus block the biotin binding pocket. Small amino acids and amino acids located at the surface such as e.g. Leu25, Ser27, Ser45 or/and Leu110 are preferably substituted by amino acids with more volume such as Arg, Trp, Tyr, Phe or His.
In order to achieve the desired binding affinity it is also possible to form muteins of streptavidin or avidin in which at least two amino acids have been substituted. In the case of streptavidin preferably at least two of the amino acids Leu25, Ser27, Ser45 and Leu110 e.g. the amino acid pairs Leu25 and Ser45, Ser27 and Ser45 or Ser45 and Leu110 are substituted by suitable amino acids especially amino acids more voluminous such as Arg, Trp, Tyr, Phe or His. It is particularly preferable to substitute Leu25 by Trp and Ser45 by Arg, Ser27 by Arg and Ser45 by Arg, Ser45 by Trp and Leu110 by Trp or Ser45 by Tyr and Leu110 by Trp.
The substitution of more than two amino acids also leads to muteins according to the invention in the case of streptavidin or avidin. In such streptavidin multiple mutants preferably at least three of the amino acids Leu25, Ser27, Ser45 and Leu110 are preferably substituted by more voluminous amino acids as defined above. In specific examples of three-fold combination mutants Leu25 was substituted by Trp, Ser45 by Trp and Leu110 by Trp or Leu25 by Trp, Ser45 by Tyr and Leu110 by Trp.
In a further preferred multiple combination mutant at least two of the amino acids Leu25, Ser27, Ser45 and Leu110 as well as additionally Trp120 are mutagenized. A specific example of such a triple mutant contains substitutions of Ser27 by Arg, Ser45 by Arg and Trp120 by Ala.
In the case of an avidin mutein one or several amino acids at positions Leu14, Ser16, Tyr33, Thr35, Val37, Thr38, Ser75, Thr77, Leu99 and Ile117 are preferably substituted. Amino acid substitutions are especially preferred at positions Leu14, Ser16, Thr35 or/and Leu99. These amino acids are preferably substituted by more voluminous amino acids such as Arg, Tyr, Trp, Phe or His. The other possibilities of substitution mentioned for streptavidin are also suitable for avidin.
The DNA sequence coding for native streptavidin is shown in SEQ ID NO.1. The respective protein sequence is shown in SEQ ID NO.2. The stated numbers of amino acids relate to this sequence. The nucleic acid sequence of native avidin is shown in SEQ ID NO.3. SEQ ID NO.4 shows the amino acid sequence of avidin. The amino acids are numbered according to this sequence.
According to the invention it is also possible to produce muteins of avidin and streptavidin variants which in their original form are capable of binding to biotin. Muteins of a shortened streptavidin (recombinant core streptavidin) are preferred according to the invention. This core streptavidin is preferably coded by the nucleotide sequence shown in SEQ ID NO. 15 and contains the amino acid sequence shown in sequence ID NO.16. The production of this core streptavidin is described in WO 93/09144. Preferred muteins of the core streptavidin contain mutations as they have already been described for native streptavidin.
A further subject matter of the present invention is a nucleic acid coding for a streptavidin or avidin mutein. This nucleic acid can for example be produced by site-specific in vitro mutagenesis of a nucleic acid according to SEQ ID NO.1, SEQ ID NO.3 or SEQ ID NO.15. The nucleic acid according to the invention can be located on a vector such as a prokaryotic plasmid preferably a plasmid which can be replicated in E. coli. The nucleic acid is located on the vector preferably in operative linkage with a promoter which allows expression in the respective host organism.
Yet a further subject matter of the invention is a cell which is transformed with a vector which contains an avidin or streptavidin mutein gene. The cell is preferably a prokaryotic cell in particular a gram-negative bacterial cell e.g. an E. coli cell.
The muteins are preferably produced by recombinant expression in a suitable host cell in particular a prokaryotic host cell such as E. coli. In this case the muteins are usually produced in the form of inactive inclusion bodies which can be renatured under suitable conditions.
The muteins can be used after renaturation and purification without further treatment in a soluble form or after immobilization on a solid phase as an interference elimination reagent. Moreover the muteins can also be used in the form of a soluble or immobilized polymer conjugate. Such polymer conjugates can be produced by chemical coupling of several mutein molecules or by coupling with other macromolecules such as polypeptides, proteins, carbohydrates etc.
Conjugates of the mutein with a further polypeptide or protein are preferred. This is especially preferably a conjugate with an albumin e.g. bovine serum albumin. The production of polymer conjugates of the muteins and optionally of further macromolecules can be carried out according to known methods (see e.g. EP-A-0 269 092).
In addition the invention concerns the use of one of the muteins described above as interference elimination reagent for assays to detect an analyte which contains the streptavidin/avidin-biotin binding pair as a test component. In this case the muteins can be used in a soluble or/and immobilized form. In one embodiment the muteins can be used together with a non-modified streptavidin/avidin solid phase in a heterogeneous assay e.g. an immunological or/and hybridization assay. In this case the muteins can be added to the test mixture in a soluble or/and immobilized form for example in the form of a separate solid phase.
The test can be carried out as a single-step or two-step process i.e. the sample to be determined can be brought into contact with the mutein and non-modified streptavidin/avidin together or in separate reaction steps.
Moreover the muteins according to the invention can also be used in other test formats e.g. in homogeneous assays, agglutination assays etc. provided that the streptavidin/avidin-biotin binding pair is present as test component. In this connection the term xe2x80x9cbiotinxe2x80x9d encompasses biotin in its free form as well as in the form of biotinylated substances such as biotinylated nucleic acids, carbohydrates, lipids, peptides or polypeptides. In addition the term also encompasses biotin analogues and biotin derivatives such as iminobiotin, desthiobiotin and streptavidin affinity peptides.
A further subject matter of the invention is an interference elimination reagent to reduce or/and avoid unspecific interactions in a method for the determination of an analyte, wherein the interference elimination reagent contains one or several of the muteins described above. This interference elimination reagent can be present in a soluble form or/and immobilized on a solid phase preferably on a membrane, a microtitre plate, a microreagent vessel or on microbeads. Substances which interact unspecifically with assay components can be captured by the interference elimination reagent which improves the test sensitivity. The interference elimination reagent has an essentially unchanged binding capacity towards interfering components compared to non-modified avidin or streptavidin so that interfering components of the test sample are effectively captured. However, in contrast to native avidin or streptavidin the interference elimination reagent has an affinity to biotin which is practically negligible for the test which is why the detection of the analyte in the test sample is not significantly influenced.
A further subject matter of the invention is a method for the qualitative and/or quantitative detection of an analyte in a test sample comprising the use of the specific binding pair streptavidin/avidin-biotin wherein a mutein of streptavidin or avidin with a binding affinity to biotin of  less than 1010 l/mol is added as an interference elimination reagent.
In one embodiment of the present invention the method is a heterogeneous assay in which the analyte is determined via binding to a solid phase, the streptavidin/avidin-binding pair being involved in this solid phase binding.
In a preferred embodiment of this test format a solid phase is used which is coated with streptavidin and to which it is intended to bind a biotinylated test component. In such a test format it is possible to add the interference elimination reagent according to the invention in a soluble or/and immobilized form. An immobilized interference elimination reagent is preferably added in the form of a separate inactive solid phase, wherein the test sample is either firstly brought into contact with the inactive solid phase alone and only later with the active solid phase or simultaneously contacted with the active and inactive solid phase.
When using a soluble interference elimination reagent it is preferable to use a single-step test in which the interference elimination reagent is present in the sample liquid together with all the other test components.
The interference elimination reagent can also successfully be used when using a biotinylated solid phase and soluble streptavidin/avidin as test components e.g. in a soluble form or in the form of a separate inactive solid phase.
The analyte in the method according to the invention can be detected in a known manner by an indirect or direct label. The detection is achieved using directly labelled detection reagents in such a way that the detection reagent for example binds to the analyte and forms a detectable complex which carries the label or binds competitively to the analyte at a specific binding site. Detection reagents with indirect labelling comprises several components, the component which binds to the analyte being unlabelled and capable of binding to a further component that carries a label.
Suitable labels are known to a person skilled in the art. For example radioactive labels, chemiluminescent, fluorescent or electrochemiluminescent labels, dyed particles such as e.g. metal sol particles or dyed or undyed latex can be used. The label can also yield an indirect signal such as e.g. enzyme labels with enzymes such as peroxidase, xcex2-galactosidase or alkaline phosphatase.
A further subject matter of the invention is a test kit to qualitatively or/and quantitatively detect an analyte in a test sample which contains a polypeptide capable of binding to biotin as well as further components of the respective assay and an interference elimination reagent which comprises a mutein according to the invention. The interference elimination reagent can be present in a soluble form or on a solid phase in particular on a microtitre plate, a microreagent vessel, a membrane or immobilized on microbeads.
A further subject matter of the invention is the use of muteins of avidin and streptavidin in which at least one amino acid of the native polypeptide is substituted and which has a binding affinity to biotin in the range of 105 to 1011 l/mol as a system that can be regenerated for binding biotinylated substances. Muteins with a binding affinity to biotin in the range of 105 to 1010 l/mol and in particular 105 to 108 l/mol are preferred.
The system that can be regenerated for binding biotinylated substances preferably comprises a solid phase on which the streptavidin muteins are immobilized. Examples of suitable solid phases are sensor chips (e.g. the Biacore system of the Kabi Pharmacia Co), reaction vessels such as polystyrene tubes or cuvettes, microtitre plates, microbeads, latex particles and support materials for affinity columns. The term xe2x80x9cbiotinylated substancesxe2x80x9d is in particular to be understood as conjugates of biotin and biotin analogues, biotin analogues being those substances which form a complex with the biotin binding pocket of (native) streptavidin or avidin such as iminobiotin, desthiobiotin and streptavidin affinity peptides.
The advantage of the solid phases that can be regenerated according to the invention in comparison to a solid phase coated with native streptavidin/avidin is that they have on the one hand an adequately high binding affinity for biotin (in the form of free biotin or biotinylated substances) so that the solid phase can be used in assays for the detection of analytes, for the investigation of receptor-ligand interactions and for the purification or analysis of biotinylated substances. On the other hand the binding affinity of the solid phase to biotin or a biotinylated substance is sufficiently low to enable a regeneration of the solid phase i.e. it is possible to detach the biotin. This detachment is preferably carried out by reducing the pH value to pH  less than 4.5 or/and by addition of chaotropic substances i.e. substances which interfere with the formation of hydrogen bridges. Alternatively the detachment for isolating the biotinylated substances can also be achieved by adding free biotin or/and biotin analogues. Gradient elution is particularly preferred.
In a preferred embodiment the solid phase capable of regeneration can be used as an affinity matrix. This affinity matrix is used to purify biotinylated substances such as biotinylated antibodies or to separate such substances based on the number of biotin residues bound per molecule. If non-modified streptavidin or avidin is used as the matrix, it is practically impossible to release the substances brought into contact with the matrix due to the high binding affinity. Attempts have been made in the state of the art to solve this problem by converting avidin into its monomers by treatment with urea or by using iminobiotin instead of biotin in order to lower the binding affinity. However, these methods are time-consuming and associated with additional problems. Using muteins according to the invention it is possible to produce affinity matrices with binding affinities to biotin which enable a reversible binding and thus recovery of the analyte.
In addition it is preferred to use the solid phase that can be regenerated according to the invention to determine receptor/ligand interactions e.g. as a coated sensor chip. The binding of molecules to this surface can for example be examined by surface plasmon resonance spectroscopy.
The plasmids and microorganisms mentioned in the present application have been deposited under the following deposit numbers at the xe2x80x9cDeutsche Sammlung von Mikroorganismen und Zellkulturen GmbHxe2x80x9d (DSM), Mascheroderweg 1B, D-30300 Braunschweig according to the rules of the Budapest treaty.
In the sequence list
SEQ ID NO.1 shows the nucleotide sequence coding for streptavidin including the sequence coding for the signal peptide
SEQ ID NO.2 shows the amino acid sequence of streptavidin including the signal sequence
SEQ ID NO.3 shows the nucleotide sequence coding for avidin including the sequence coding for the signal peptide
SEQ ID NO.4 shows the protein sequence of avidin including the signal sequence
SEQ ID NO.5 shows the nucleotide sequence of primer N1,
SEQ ID NO.6 shows the nucleotide sequence of primer N2,
SEQ ID NO.7 shows the nucleotide sequence of primer N3,
SEQ ID NO.8 shows the nucleotide sequence of primer N4,
SEQ ID NO.9 shows the nucleotide sequence of primer N5,
SEQ ID NO.10 shows the nucleotide sequence of primer N6,
SEQ ID NO.11 shows the nucleotide sequence of primer N7,
SEQ ID NO.12 shows the nucleotide sequence of primer N8,
SEQ ID NO.13 shows the nucleotide sequence of primer N9,
SEQ ID NO.14 shows the nucleotide sequence of primer N10,
SEQ ID NO.15 shows the nucleotide sequence coding for core streptavidin according to WO 93/09144 and
SEQ ID NO.16 shows the amino acid sequence of core streptavidin.